trackplot 0.2.2__tar.gz → 0.2.3__tar.gz

{trackplot-0.2.2 → trackplot-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: trackplot
-Version: 0.2.2
+Version: 0.2.3
 Home-page: https://github.com/ygidtu/trackplot
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
@@ -211,5 +211,5 @@ contact [Yiming Zhang](https://github.com/ygidtu) and
 
 If you use Sashimi.py in your publication, please cite Sashimi.py by
 
-[Zhang et al. Sashimi.py: a flexible toolkit for combinatorial analysis of genomic data. bioRxiv 2022.11.02.514803.](https://www.biorxiv.org/content/10.1101/2022.11.02.514803v1)
+[Zhang et al. bioRxiv, 2022.11.02.514803.](https://www.biorxiv.org/content/10.1101/2022.11.02.514803v1)
 

{trackplot-0.2.2 → trackplot-0.2.3}/README.md

@@ -203,5 +203,5 @@ contact [Yiming Zhang](https://github.com/ygidtu) and
 
 If you use Sashimi.py in your publication, please cite Sashimi.py by
 
-[Zhang et al. Sashimi.py: a flexible toolkit for combinatorial analysis of genomic data. bioRxiv 2022.11.02.514803.](https://www.biorxiv.org/content/10.1101/2022.11.02.514803v1)
+[Zhang et al. bioRxiv, 2022.11.02.514803.](https://www.biorxiv.org/content/10.1101/2022.11.02.514803v1)
 

{trackplot-0.2.2 → trackplot-0.2.3}/setup.py

@@ -2,7 +2,7 @@ import os
 from configparser import ConfigParser
 from setuptools import setup, find_packages
 
-__version__ = "0.2.2"
+__version__ = "0.2.3"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

{trackplot-0.2.2 → trackplot-0.2.3}/trackplot/base/ReadDepth.py

@@ -57,11 +57,15 @@ class ReadDepth(object):
 
     @property
     def plus(self) -> Optional[np.array]:
-        return self._plus_ / self._number_of_merged_
+        if self._plus_ is not None and self._number_of_merged_ > 0:
+            return self._plus_ / self._number_of_merged_
+        return self._plus_
 
     @property
     def minus(self) -> Optional[np.array]:
-        return self._minus_ / self._number_of_merged_
+        if self._minus_ is not None and self._number_of_merged_ > 0:
+            return self._minus_ / self._number_of_merged_
+        return self._minus_
 
     @property
     def wiggle(self) -> np.array:

{trackplot-0.2.2 → trackplot-0.2.3}/trackplot/cli.py

@@ -21,7 +21,7 @@ from trackplot.conf.config import CLUSTERING_METHOD, COLORS, COLORMAP, DISTANCE_
 from trackplot.file.ATAC import ATAC
 from trackplot.plot import Plot
 
-__version__ = "0.2.2"
+__version__ = "0.2.3"
 __author__ = "ygidtu & Ran Zhou"
 __email__ = "ygidtu@gmail.com"
 

{trackplot-0.2.2 → trackplot-0.2.3}/trackplot/file/Reference.py

@@ -335,18 +335,14 @@ class Reference(File):
                     keep_original=True
                 )
             except OSError as err:
-                logger.error(err)
-                logger.error("Guess gtf needs to be sorted")
+                logger.warning(f"Guess gtf needs to be sorted: {err}")
 
                 sorted_gtf = re.sub(r"\.gtf(.gz)?$", "", input_gtf) + ".sorted.gtf.gz"
                 if os.path.exists(sorted_gtf) and os.path.exists(sorted_gtf + ".tbi"):
                     return sorted_gtf
 
                 cls.sort_gtf(input_gtf, sorted_gtf)
-                pysam.tabix_index(
-                    sorted_gtf, preset="gff",
-                    force=True, keep_original=True
-                )
+                pysam.tabix_index(sorted_gtf, preset="gff", force=True, keep_original=True)
                 return sorted_gtf
         elif os.path.getctime(output_gtf) < os.path.getctime(output_gtf):
             logger.info("the tbi index is older than the gtf file")
@@ -442,11 +438,9 @@ class Reference(File):
                 )
                 transcripts[t] = transcripts.get(t, 0) + 1
         except IOError as err:
-            logger.error('There is no .bam file at {0}'.format(self.path))
-            logger.error(err)
+            logger.warning(f"There is no .bam file at {self.path}: {err}")
         except ValueError as err:
-            logger.error(self.path)
-            logger.error(err)
+            logger.warning(f"{self.path}: {err}")
 
         return sorted([x for x, y in transcripts.items() if y > threshold_of_reads])
 
@@ -502,11 +496,9 @@ class Reference(File):
                 transcripts.append(read)
 
         except IOError as err:
-            logger.error('There is no .bed file at {0}'.format(self.path))
-            logger.error(err)
+            logger.warning(f"There is no .bed file at {self.path}: {err}")
         except ValueError as err:
-            logger.error(self.path)
-            logger.error(err)
+            logger.warning(f"{self.path}: {err}")
         return transcripts
 
     def load(self, region: GenomicLoci, threshold_of_reads: int = 0, **kwargs):

{trackplot-0.2.2 → trackplot-0.2.3}/trackplot.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: trackplot
-Version: 0.2.2
+Version: 0.2.3
 Home-page: https://github.com/ygidtu/trackplot
 Requires-Python: >=3.8
 Description-Content-Type: text/markdown
@@ -211,5 +211,5 @@ contact [Yiming Zhang](https://github.com/ygidtu) and
 
 If you use Sashimi.py in your publication, please cite Sashimi.py by
 
-[Zhang et al. Sashimi.py: a flexible toolkit for combinatorial analysis of genomic data. bioRxiv 2022.11.02.514803.](https://www.biorxiv.org/content/10.1101/2022.11.02.514803v1)
+[Zhang et al. bioRxiv, 2022.11.02.514803.](https://www.biorxiv.org/content/10.1101/2022.11.02.514803v1)